5Z15 | pdb_00005z15

Crystal structure of human TLR8 in complex with CU-CPT9c

PDB DOI: https://doi.org/10.2210/pdb5Z15/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2017-12-25 Released: 2018-07-04
Deposition Author(s): Tanji, H., Ohto, U., Shimizu, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.289 (Depositor), 0.285 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Inhibition of Toll-like Receptor 8 by Specifically Targeting a Unique Allosteric Site and Locking Its Resting State

Hu, Z., Zhang, S., Tanji, H., Jiang, S., Li, J., Sakaniwa, K., Jin, J., Bian, Y., Ohto, U., Shimizu, T., Yin, H.

To be published.

Macromolecule Content

Total Structure Weight: 191.28 kDa
Atom Count: 12,314
Modeled Residue Count: 1,481
Deposited Residue Count: 1,622
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 8	A, B	811	Homo sapiens	Mutation(s): 0 Gene Names: TLR8, UNQ249/PRO286
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR97 (Homo sapiens) Explore Q9NR97 Go to UniProtKB: Q9NR97
PHAROS: Q9NR97 GTEx: ENSG00000101916
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NR97
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9NR97-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G	2		N-Glycosylation	Interactions Focus chain D Focus chain G Interactions & Density Focus chain D Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	5		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H	4		N-Glycosylation	Interactions Focus chain F Focus chain H Interactions & Density Focus chain F Focus chain H
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7VL Query on 7VL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain I [auth A] MOL2 format, chain N [auth A] MOL2 format, chain I [auth A] mmCIF format, chain N [auth A] mmCIF format, chain I [auth A]	I [auth A], N [auth A]	4-(7-chloranylquinolin-4-yl)-2-methyl-phenol C₁₆ H₁₂ Cl N O VBXAMTUJCKJXCI-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth A] Interactions & Density Focus chain I [auth A] Focus chain N [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.289 (Depositor), 0.285 (DCC)
R-Value Work: 0.202 (Depositor), 0.202 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.892	α = 90
b = 98.747	β = 109.04
c = 139.476	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-07-04

Deposition Author(s):

Tanji, H.

Ohto, U.

Shimizu, T.

Revision History (Full details and data files)

Version 1.0: 2018-07-04
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-13
Changes: Data collection, Database references, Structure summary